A Pilot Study of Next-Generation Sequencing on Cell-Free DNA from Blood Plasma and Bone Marrow Fluid for Detecting Leukemic Clonal Abnormalities

Abstract

Next-generation sequencing on maternal plasma cell-free DNA (cfDNA) has been applied to non-invasive prenatal screening for common aneuploidy in the fetuses. It has been proposed that cfDNA could be a useful biomarker for early cancer detection, residual disease discovery, and chemotherapy monitoring. In patients with hematological malignancies, the cancerous cells undergoing apoptosis could release leukemic cfDNA into the blood plasma or bone marrow fluid, and the chromosomal profiling from those cfDNA could be used to detect clonal chromosome abnormalities. To evaluate the technical and clinical feasibility of next-generation sequencing on cfDNA for detecting leukemic clonal abnormalities, a pilot study was performed on ten residual samples to compare results from cfDNA sequencing analysis (cfDSA) with diagnostic findings from karyotyping, fluorescence in situ hybridization (FISH) and array comparative genomic hybridization (aCGH). Six of the ten samples had normal karyotypes, and consistently, both cfDSA and aCGH showed normal results. In three samples with different clonal chromosome abnormalities, aCGH and cfDSA detected comparable copy number aberrations and further defined the chromosomal abnormalities. In one case with FISH-detected deletions of 7q and 20q in 11-12% of cells, neither cfDSA nor aCGH detected any copy number aberrations. The result from this pilot study demonstrated that leukemic cfDNA in the blood plasma, and possibly bone marrow fluid, could be used to detect clonal chromosome abnormalities. However, the analytic and clinical validities need to be established using a large sample series and user-friendly designed bioinformatic tools need to be developed for robust sequencing data analysis in a clinical setting.